Variant report

Variant	rs6894687
Chromosome Location	chr5:112742953-112742954
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10035686	0.82[AMR][1000 genomes]
rs10041899	0.88[AMR][1000 genomes]
rs10042223	0.92[CHB][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes]
rs10051115	0.82[CEU][hapmap]
rs10051834	0.92[CHB][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes]
rs10053654	0.88[AMR][1000 genomes]
rs10061331	0.83[AMR][1000 genomes]
rs10062004	0.87[YRI][hapmap];0.88[AMR][1000 genomes]
rs10074214	0.82[ASW][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes]
rs10900685	0.88[YRI][hapmap]
rs1116547	0.84[YRI][hapmap]
rs1120091	0.82[AMR][1000 genomes]
rs11241201	0.92[YRI][hapmap]
rs11241206	0.96[YRI][hapmap]
rs11738075	0.87[YRI][hapmap]
rs11738215	0.88[YRI][hapmap]
rs12514091	0.81[YRI][hapmap]
rs12516418	0.87[YRI][hapmap]
rs12523255	0.95[YRI][hapmap]
rs13157609	0.82[AMR][1000 genomes]
rs13181534	0.82[CEU][hapmap]
rs13188946	0.82[ASW][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes]
rs13359330	0.86[AMR][1000 genomes]
rs1366393	0.88[ASW][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes]
rs1464163	0.83[AMR][1000 genomes]
rs1517207	0.88[AMR][1000 genomes]
rs17135608	0.91[YRI][hapmap]
rs1845291	0.82[AMR][1000 genomes]
rs1850407	0.82[ASW][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.89[MEX][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes]
rs1850410	0.84[YRI][hapmap]
rs1850412	0.82[ASW][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes]
rs1965429	0.83[MEX][hapmap]
rs2222144	0.92[CHB][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes]
rs255861	0.84[AMR][1000 genomes]
rs255862	0.86[AMR][1000 genomes]
rs255865	0.84[AMR][1000 genomes]
rs255866	0.86[AMR][1000 genomes]
rs255877	0.86[AMR][1000 genomes]
rs26959	0.94[ASW][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs26961	0.86[CHB][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs26964	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs26966	0.85[CHB][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs26967	0.85[AMR][1000 genomes]
rs26968	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs26969	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs27567	0.94[ASW][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4331889	0.92[CHB][hapmap];0.92[YRI][hapmap]
rs4705814	0.83[YRI][hapmap]
rs6594701	1.00[CHB][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes]
rs6594703	0.86[YRI][hapmap];0.83[AMR][1000 genomes]
rs6594704	0.92[CHB][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes]
rs6594705	0.92[CHB][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes]
rs6594707	0.84[YRI][hapmap];0.88[AMR][1000 genomes]
rs6594710	0.82[ASW][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes]
rs6594712	0.92[CHB][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes]
rs6594713	0.82[CEU][hapmap]
rs6594714	0.82[CEU][hapmap]
rs6860495	0.88[AMR][1000 genomes]
rs6861668	0.82[AMR][1000 genomes]
rs6864528	0.92[YRI][hapmap]
rs6867397	0.82[ASW][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes]
rs6868141	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6868148	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6870401	0.82[CEU][hapmap]
rs6871812	0.88[AMR][1000 genomes]
rs6876848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6877524	0.84[YRI][hapmap]
rs6880552	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880749	0.83[AMR][1000 genomes]
rs6883547	0.86[GIH][hapmap]
rs6887482	0.82[CEU][hapmap]
rs7700413	0.83[AMR][1000 genomes]
rs7708084	0.92[CHB][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes]
rs7714734	0.88[AMR][1000 genomes]
rs7714760	0.89[CEU][hapmap]
rs7717000	0.88[YRI][hapmap]
rs7717422	0.86[CHB][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes]
rs7718480	0.83[AMR][1000 genomes]
rs7725589	0.92[CHB][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes]
rs7729269	0.82[CEU][hapmap];0.84[GIH][hapmap]
rs7731231	0.82[CEU][hapmap]
rs7731465	0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs7731854	0.84[AMR][1000 genomes]
rs7734061	0.88[AMR][1000 genomes]
rs7734304	0.88[AMR][1000 genomes]
rs9326884	0.88[AMR][1000 genomes]
rs9326886	0.86[CHB][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes]
rs9326887	0.85[CHB][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes]
rs9326888	0.86[CHB][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes]
rs9326889	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9632462	0.84[YRI][hapmap];0.88[AMR][1000 genomes]
rs9687632	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6894687	YTHDC2	cis	cerebellum	SCAN
rs6894687	YTHDC2	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112724400-112751200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:112741400-112746400	Weak transcription	Pancreas	Pancrea
3	chr5:112742200-112743800	Enhancers	Fetal Heart	heart

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